Select Effects 1.0
Select Effects is an Adobe Illustrator plugin which allows you to select art objects with transparency.Comercialware

FadingWindow 1.0
FadingWindow is a REALbasic class which provides a window subclass that can set it's own transparency.Freeware

X-ray for Adobe InDesign/InCopy 1.0.1
Is 21'' screen still too small to fit all the useful panels and see the layout at the same time? Are you considering buying second screen and using it just to store the panels?
Before you spend money on a new screen, try X-ray.Demo

Lucid 1.2
Now you can add the new transparent window feature introduced with WindowsFreeware